The proteasome is a large protein complex that contains 33 distinct subunits. Proteasome complexes function as proteases in part to degrade unneeded or misfolded proteins. Proteasomes regulate many aspects of cell physiology, and proteasome dysfunction has been implicated in a variety of diseases, including cancer and neurodegenerative diseases (Finley D., (2009), Annu Rev. Biochem., 78, 477-513; Hoeller and Dikic, (2009), Nature, 458, 438-444; Demarto and Gillette, (2007), Cell, 129, 659-662); Dahlmann, B. (2007) BCB Biochem 8, Suppl 1, S3; Schartz A L and Ciechanover A (2009) Ann Rev Pharmacol Toxicol 49, 73-96).
Most, but not all, proteasome substrates are targeted for degradation via the covalent attachment of multimeric chains of a small, highly-conserved protein called ubiquitin. Because longer ubiquitin chains interact more strongly with the proteasome than shorter chains (Thrower et al. (2000), EMBO J. 19, 94-102), processes that alter ubiquitin chain length frequently also affect substrate degradation rates. The length of ubiquitin chains attached to substrates tagged for proteasome degradation can be modulated by certain proteasome-associated deubiquitinating enzymes and ubiquitin ligases. These deubiquitinating enzymes and ligases appear to regulate proteasome activity by disassembling or extending proteasome-bound ubiquitin chains.
Mammalian proteasomes contain three major deubiquitinating enzymes: Rpn11, Uch37, and Usp14 (Finley D., (2009), Annu Rev. Biochem., 78, 477-513). Rpn11 removes ubiquitin from the tagged substrate by cutting at the junction between the ubiquitin chain and the substrate. Because the Rpn11-mediated cleavage occurs following a substrate's commitment to proteolysis, but prior to substrate degradation, Rpn11 helps to prevent ubiquitin from being degraded along with the substrate, thus minimizing fluctuations in cellular ubiquitin levels. Additionally, because the proteasome substrate must pass through a narrow translocation channel before encountering the proteasome's sequestered proteolytic sites, removal of a bulky ubiquitin chain may also facilitate substrate translocation. Thus, removal of the ubiquitin chain by Rpn11 promotes substrate degradation through en bloc removal of the ubiquitin chain at a relatively late step in the proteasome pathway (Verma et al., (2002) Science, 298, 611-615; Yao and Cohen, (2002), Nature, 419, 403-407).
In contrast to Rpn11, Uch37 functions prior to the commitment of a substrate to proteasome degradation. Uch37 disassembles ubiquitin chains at the substrate-distal tip (Lam et al., (1997), Nature, 385, 737-740), and its enzymatic activity shortens chains rather than remove them entirely. It has been proposed that chain trimming by Uch37 increases the ability of the proteasome to discriminate between long and short multiubiquitin chains (Lam et al., (1997), Nature, 385, 737-740). Little is known about how Uch37 may regulate proteasome function in cells.
Very little is known about the function of Usp14. However, the yeast ortholog of Usp14, Ubp6, has been suggested to disassemble ubiquitin chains at the substrate-distal tip and to function prior to the commitment of a substrate to proteasome degradation. (Hanna et al., (2006), Cell, 127(7), 1401-1413). Ubp6 is thought to act as a proteasome inhibitor, and prior work on Ubp6 has indicated a noncatalytic mode of proteasome inhibition (Hanna et al., (2006), Cell, 127(7), 1401-1413).